Kakuna is still one of the most interesting Bugs out there. I expect it to be Underused for a while as people drool over sweepers like Scizor and Azelf, and then returned to as people go back for the old reliable standards. Overall, Kakuna hasn't changed much, but it didn't really need to. That said, it got a few new toys in terms of moves and items. Expect to see Kakuna work the same way it did in Advance.
With Kakuna's new Bug Bite, it's justifiable that it has moved up to the NFE (Notoriously Freaking Epic) tier. (Seriously, who thinks of the names for these tiers, anyway?) With this new, extremely useful move under its shell, Kakuna has the ability to effectively shape its tier to its personal needs.
As the standard, this is easily the most popular Kakuna set.
Iron Defense increases its already high Defense. String Shot can be used to try and mediate quicker things such as Weavile and Dugtrio. Bug Bite is a solid move to use—as Kakuna's most powerful STAB—and is useful to nab a Ganlon or Apicot Berry, both of which will help Kakuna take hits more easily. Black Sludge is an option to not only heal Kakuna, but to help ward off use of Trick or Covet. It is important to note, however, that if you opt for Black Sludge, your opponent can cripple one of your other teammates by Tricking it on to them.
The given EVs provide a good balance between offense and defense, as well as allowing Kakuna to take physical hits quite well.
A sweeping set. Iron Defense a few times, then sweep with Bug Bite—Kakuna's most reliable STAB option—using the Metronome. Be careful about Steel-types switching in, as they easily counter this set. Poison Sting is for an additional STAB option, though you'll usually be using Bug Bite. With Metronome, make sure to stick with the same attack, as your Metronome boost will eventually equal the boost given even by a Choice Band by spamming the same attack repetitively.
This is your standard Choice sweeper. With Bug Bite, Kakuna is not walled by the likes of Steelix and Steel-type Arceus. As a matter of fact, Bug Bite's addition lowers max HP / max Def Steelix from a 94HKO to a 36HKO. Max HP Steel-type Arceus is now a 25 HKO, while min HP/Def Psychic Arceus is a 22HKO.
With Jolly and a Choice Scarf, Kakuna outruns anything slower than Heatran, but if it manages to bite a Salac Berry off of some unsuspecting opponent, it gets boosted up to under Ninjask, allowing for a fast physical sweeper. Without the Attack boost from Adamant and Choice Band, you get a 45HKO on Steelix. In 2 vs. 2, pair it up with something with a Salac Berry and Bug Bite the Berry to receive the extra Speed boost.
This Kakuna is mainly a Trapinch and Dugtrio counter, though it will also work against Wobbuffet if you're willing to use Kakuna in Ubers. Use String Shot to decrease Dugtrio's Speed, possibly hit it with poison status from Poison Sting, and then switch out using Shed Shell. Wobbuffet especially hates being poisoned, but watch out for Encore. If the enemy Wobbuffet Encores your String Shot, they can switch in an already slow sweeper, such as Tyranitar or Rhyperior; a locked Poison Sting makes way for an entrance by a Steel-type, such as Metagross or Dialga.
The old in-game standard. It's as good of a tank as it ever was. With the inclusion of Sticky Barb, it now has an opportunity to deal damage better and faster than it could before. This set works better with Leech Seed, Toxic Spikes, and/or other residual damage support.
The given EVs maximize Kakuna's ability to take physical hits.
Kakuna's movepool is rather shallow; however, it still has a couple different choices. A Lum Berry can be used should Kakuna accidentally switch into Hypnosis. Type-resist Berries can also be useful. The big three that will help Kakuna are Charti, Coba, and Occa. Charti will reduce damage inflicted from Rock-type attacks, Coba the same with Flying, while Occa will do the trick for Fire. Occa is most helpful when considering the widespread usage of Heatran and Infernape. Rock- and Flying-type attacks are much less common.
Checks and Counters
Parasect can kill it, but it has to be careful switching in because of Bug Bite and Poison Sting. Farfetch'd resists its moves, but can be walled by Iron Defense. Thief Banette with Frisk also causes some problems by selectively stealing items while snatching away Kakuna's Iron Defenses.
Steelix and Steel-type Arceus, although somewhat manageable thanks to Bug Bite, still cause problems for our cocooned friend. Other Steel-types, such as Dialga, give Kakuna issues. Luckily, the Steel / Psychic-typed Pokemon are neutral to Bug-type attacks, meaning that Kakuna can ravage them with a powerful STAB Bug Bite.